.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data18.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : yes . Number of random starting trees : 5 . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 417 patterns found. (out of a total of 500 sites) . 78 sites without polymorphism (15.60%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -24238.6878] [GTR parameters ] . ( 1 sec) [ -23851.2542] [Alpha ][ 0.500960] . ( 1 sec) [ -23531.2435] [ 4176] [depth= 5] . ( 1 sec) [ -23394.7100] [ 4143] [depth= 3] . ( 1 sec) [ -22671.8788] [ 4097] [depth= 5] . ( 1 sec) [ -22585.8842] [ 4088] [depth= 5] . ( 1 sec) [ -22416.5410] [ 4009] [depth= 1] . ( 1 sec) [ -22273.4742] [ 3995] [depth= 4] . ( 1 sec) [ -22157.5467] [ 3975] [depth= 5] . ( 1 sec) [ -22103.4780] [ 4022] [depth= 1] . ( 1 sec) [ -21666.7525] [ 3951] [depth= 2] . ( 1 sec) [ -21607.2019] [ 3921] [depth= 1] . ( 1 sec) [ -17479.7310] [ 3778] [depth= 6] . ( 1 sec) [ -17347.5720] [ 3701] [depth= 7] . ( 2 sec) [ -16309.0512] [ 3540] [depth= 9] . ( 2 sec) [ -16071.3601] [ 3538] [depth= 2] . ( 2 sec) [ -16067.2275] [ 3538] [depth= 1] . ( 2 sec) [ -16024.7796] [ 3524] [depth= 1] . ( 2 sec) [ -15999.5303] [ 3514] [depth= 2] . ( 2 sec) [ -15820.2128] [ 3485] [depth= 3] . ( 2 sec) [ -15139.9905] [ 3482] [depth= 2] . ( 2 sec) [ -14981.1997] [ 3427] [depth= 4] . ( 2 sec) [ -14697.5800] [ 3433] [depth= 6] . ( 2 sec) [ -14439.4734] [ 3428] [depth= 1] . ( 2 sec) [ -14068.2579] [ 3401] [depth= 7] . ( 2 sec) [ -14053.0397] [ 3407] [depth= 8] . ( 2 sec) [ -13964.0162] [ 3323] [depth= 1] . ( 2 sec) [ -13567.5059] [ 3288] [depth= 9] . ( 2 sec) [ -13269.0707] [ 3169] [depth= 8] . ( 2 sec) [ -13226.7879] [ 3167] [depth= 1] . ( 2 sec) [ -12988.0907] [ 3069] [depth= 2] . ( 2 sec) [ -12965.3623] [ 3064] [depth= 1] . ( 2 sec) [ -12801.5722] [ 2974] [depth= 7] . ( 2 sec) [ -12774.0369] [ 2976] [depth= 1] . ( 2 sec) [ -12662.7708] [ 2945] [depth= 9] . ( 2 sec) [ -12593.4026] [ 2930] [depth= 2] . ( 2 sec) [ -12507.5523] [ 2899] [depth= 1] . ( 2 sec) [ -12500.6391] [ 2901] [depth= 1] . ( 3 sec) [ -12335.1983] [ 2890] [depth= 10] . ( 3 sec) [ -12325.9075] [ 2885] [depth= 1] . ( 3 sec) [ -11886.6496] [ 2792] [depth= 16] . ( 3 sec) [ -11870.2842] [ 2793] [depth= 1] . ( 3 sec) [ -11857.0459] [ 2790] [depth= 7] . ( 3 sec) [ -11763.7108] [ 2767] [depth= 2] . ( 3 sec) [ -11704.0820] [ 2751] [depth= 2] . ( 3 sec) [ -11440.8974] [ 2753] [depth= 1] . ( 3 sec) [ -11285.4768] [ 2660] [depth= 4] . ( 3 sec) [ -11255.8128] [ 2651] [depth= 6] . ( 3 sec) [ -11021.2316] [ 2557] [depth= 6] . ( 3 sec) [ -11007.9766] [ 2554] [depth= 2] . ( 3 sec) [ -10935.8157] [ 2547] [depth= 1] . ( 3 sec) [ -10921.5310] [ 2539] [depth= 1] . ( 3 sec) [ -10906.7516] [ 2537] [depth= 1] . ( 3 sec) [ -10873.8300] [ 2527] [depth= 1] . ( 3 sec) [ -10681.6344] [ 2461] [depth= 5] . ( 3 sec) [ -10655.7024] [ 2466] [depth= 2] . ( 3 sec) [ -10612.4179] [ 2441] [depth= 7] . ( 3 sec) [ -10284.9129] [ 2365] [depth= 3] . ( 4 sec) [ -10199.8208] [ 2358] [depth= 13] . ( 4 sec) [ -10012.8357] [ 2341] [depth= 1] . ( 4 sec) [ -9962.7574] [ 2245] [depth= 1] . ( 4 sec) [ -9946.7766] [ 2248] [depth= 2] . ( 4 sec) [ -9924.6250] [ 2245] [depth= 1] . ( 4 sec) [ -9846.5004] [ 2229] [depth= 2] . ( 4 sec) [ -9622.4527] [ 2136] [depth= 10] . ( 4 sec) [ -9597.8465] [ 2130] [depth= 1] . ( 4 sec) [ -9596.2965] [ 2129] [depth= 1] . ( 4 sec) [ -9561.6879] [ 2119] [depth= 1] . ( 4 sec) [ -9546.1613] [ 2112] [depth= 1] . ( 4 sec) [ -9500.4855] [ 2110] [depth= 2] . ( 4 sec) [ -9359.0727] [ 2074] [depth= 1] . ( 4 sec) [ -9358.6659] [ 2075] [depth= 1] . ( 4 sec) [ -9221.6075] [ 2011] [depth= 1] . ( 4 sec) [ -9213.3410] [ 2017] [depth= 1] . ( 4 sec) [ -9152.6500] [ 2008] [depth= 2] . ( 4 sec) [ -9146.8532] [ 2012] [depth= 1] . ( 5 sec) [ -9075.6704] [ 1978] [depth= 1] . ( 5 sec) [ -8943.8349] [ 1936] [depth= 5] . ( 5 sec) [ -8830.0159] [ 1930] [depth= 1] . ( 5 sec) [ -8804.6983] [ 1919] [depth= 3] . ( 5 sec) [ -8803.5709] [ 1923] [depth= 1] . ( 5 sec) [ -8770.3504] [ 1937] [depth= 1] . ( 5 sec) [ -8740.8246] [ 1916] [depth= 1] . ( 5 sec) [ -8486.3035] [Branch lengths ] . ( 6 sec) [ -8484.9616] [GTR parameters ] . ( 6 sec) [ -8455.2973] [Alpha ][ 0.889685] . ( 6 sec) [ -8410.0618] [ 1883] [depth= 3] . ( 6 sec) [ -8403.5382] [ 1865] [depth= 2] . ( 6 sec) [ -8403.4713] [ 1866] [depth= 1] . ( 6 sec) [ -8354.6245] [ 1836] [depth= 4] . ( 6 sec) [ -8345.7331] [ 1832] [depth= 1] . ( 6 sec) [ -8336.8129] [ 1830] [depth= 3] . ( 6 sec) [ -8335.1921] [ 1827] [depth= 1] . ( 7 sec) [ -8334.9836] [ 1827] [depth= 1] . ( 7 sec) [ -8329.3473] [ 1815] [depth= 1] . ( 7 sec) [ -8328.2307] [ 1815] [depth= 1] . ( 7 sec) [ -8328.0109] [ 1816] [depth= 1] . ( 7 sec) [ -8323.7064] [ 1801] [depth= 1] . ( 7 sec) [ -8323.2688] [ 1801] [depth= 1] . ( 7 sec) [ -8322.3334] [ 1797] [depth= 1] . ( 7 sec) [ -8318.7043] [ 1798] [depth= 1] . ( 7 sec) [ -8317.7483] [ 1798] [depth= 1] . ( 8 sec) [ -8314.8881] [ 1801] [depth= 1] . ( 8 sec) [ -8305.5395] [ 1811] [depth= 1] . ( 9 sec) [ -8288.2504] [Branch lengths ] . ( 10 sec) [ -8288.0119] [GTR parameters ] . ( 10 sec) [ -8286.6666] [Alpha ][ 1.010672] . ( 10 sec) [ -8283.2810] [ 1811] [depth= 1] . ( 13 sec) [ -8282.2852] [Branch lengths ] . ( 14 sec) [ -8282.2264] [GTR parameters ] . ( 14 sec) [ -8282.1959] [Alpha ][ 1.031051] . ( 14 sec) [ -8282.1271] [ 1808] [depth= 1] . ( 17 sec) [ -8281.7098] [Branch lengths ] . ( 18 sec) [ -8281.7089] [GTR parameters ] . ( 18 sec) [ -8281.7076] [Alpha ][ 1.035242] . ( 38 sec) [ -8281.6902] [Branch lengths ] . ( 38 sec) [ -8281.6902] [Topology ] . ( 39 sec) [ -8281.6886] [Topology ] . ( 40 sec) [ -8281.6881] [Topology ] . ( 40 sec) [ -8281.6880] [GTR parameters ] . ( 40 sec) [ -8281.6880] [Alpha ][ 1.035242] . ( 40 sec) [ -8281.6880] [Topology ] . ( 41 sec) [ -8281.6878] [Topology ] . ( 41 sec) [ -8281.6878] [GTR parameters ] . ( 41 sec) [ -8281.6878] [Alpha ][ 1.035242] . Checking for NNIs, optimizing five branches... . ( 47 sec) [ -8281.6573] [Topology ] . Checking for NNIs, optimizing five branches... . ( 53 sec) [ -8281.6569] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8281.656917. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -20730.7192] [GTR parameters ] . ( 1 sec) [ -20323.1644] [Alpha ][ 0.500960] . ( 1 sec) [ -20308.6638] [ 4141] [depth= 9] . ( 1 sec) [ -20068.4594] [ 4083] [depth= 11] . ( 1 sec) [ -20013.5660] [ 4062] [depth= 3] . ( 1 sec) [ -19759.5870] [ 4051] [depth= 2] . ( 1 sec) [ -19648.1728] [ 3989] [depth= 2] . ( 1 sec) [ -19586.5287] [ 3975] [depth= 6] . ( 1 sec) [ -19405.2559] [ 3941] [depth= 3] . ( 1 sec) [ -19132.7524] [ 3862] [depth= 1] . ( 1 sec) [ -18697.8251] [ 3796] [depth= 2] . ( 1 sec) [ -18342.6611] [ 3750] [depth= 12] . ( 1 sec) [ -18274.3804] [ 3745] [depth= 1] . ( 1 sec) [ -18089.1791] [ 3717] [depth= 9] . ( 1 sec) [ -18014.7406] [ 3725] [depth= 3] . ( 1 sec) [ -17666.9630] [ 3601] [depth= 4] . ( 1 sec) [ -17565.6084] [ 3595] [depth= 14] . ( 1 sec) [ -17291.3008] [ 3490] [depth= 9] . ( 2 sec) [ -16630.9608] [ 3485] [depth= 4] . ( 2 sec) [ -16567.2249] [ 3480] [depth= 1] . ( 2 sec) [ -16420.0870] [ 3475] [depth= 1] . ( 2 sec) [ -16271.1831] [ 3434] [depth= 4] . ( 2 sec) [ -16121.0561] [ 3340] [depth= 17] . ( 2 sec) [ -15742.6315] [ 3328] [depth= 2] . ( 2 sec) [ -15695.1830] [ 3331] [depth= 3] . ( 2 sec) [ -15669.9956] [ 3323] [depth= 2] . ( 2 sec) [ -14317.9193] [ 3198] [depth= 16] . ( 2 sec) [ -13965.5923] [ 3195] [depth= 4] . ( 2 sec) [ -12908.8075] [ 3037] [depth= 6] . ( 2 sec) [ -12637.4841] [ 2937] [depth= 3] . ( 2 sec) [ -12635.5916] [ 2937] [depth= 1] . ( 2 sec) [ -12603.6764] [ 2906] [depth= 6] . ( 2 sec) [ -12336.9630] [ 2895] [depth= 1] . ( 2 sec) [ -12165.7467] [ 2839] [depth= 10] . ( 2 sec) [ -11796.8656] [ 2729] [depth= 1] . ( 2 sec) [ -11662.0578] [ 2699] [depth= 9] . ( 2 sec) [ -11473.9084] [ 2618] [depth= 9] . ( 2 sec) [ -11386.3099] [ 2547] [depth= 1] . ( 2 sec) [ -11342.7917] [ 2532] [depth= 6] . ( 3 sec) [ -11195.1539] [ 2530] [depth= 1] . ( 3 sec) [ -10992.4582] [ 2475] [depth= 6] . ( 3 sec) [ -10834.6332] [ 2477] [depth= 1] . ( 3 sec) [ -10489.3887] [ 2362] [depth= 3] . ( 3 sec) [ -10486.7373] [ 2370] [depth= 1] . ( 3 sec) [ -10432.0812] [ 2354] [depth= 2] . ( 3 sec) [ -10399.6953] [ 2344] [depth= 1] . ( 3 sec) [ -10385.8350] [ 2340] [depth= 1] . ( 3 sec) [ -10364.8853] [ 2355] [depth= 11] . ( 3 sec) [ -10278.1854] [ 2350] [depth= 2] . ( 3 sec) [ -10024.3546] [ 2259] [depth= 3] . ( 3 sec) [ -9933.2472] [ 2245] [depth= 1] . ( 3 sec) [ -9804.5735] [ 2184] [depth= 1] . ( 3 sec) [ -9802.5280] [ 2185] [depth= 1] . ( 3 sec) [ -9751.7573] [ 2189] [depth= 1] . ( 3 sec) [ -9726.4718] [ 2184] [depth= 1] . ( 3 sec) [ -9713.0779] [ 2173] [depth= 1] . ( 3 sec) [ -9598.2467] [ 2146] [depth= 1] . ( 3 sec) [ -9569.1753] [ 2140] [depth= 5] . ( 4 sec) [ -9551.4236] [ 2140] [depth= 1] . ( 4 sec) [ -9502.3138] [ 2141] [depth= 2] . ( 4 sec) [ -9489.3411] [ 2141] [depth= 2] . ( 4 sec) [ -9472.1146] [ 2141] [depth= 1] . ( 4 sec) [ -9470.6301] [ 2136] [depth= 1] . ( 4 sec) [ -9468.2571] [ 2134] [depth= 1] . ( 4 sec) [ -9460.6997] [ 2135] [depth= 1] . ( 4 sec) [ -9324.4389] [ 2130] [depth= 1] . ( 4 sec) [ -9280.4699] [ 2061] [depth= 2] . ( 4 sec) [ -9237.8772] [ 2059] [depth= 3] . ( 4 sec) [ -9169.7859] [ 2046] [depth= 1] . ( 4 sec) [ -9167.1187] [ 2046] [depth= 1] . ( 4 sec) [ -8988.9048] [ 1990] [depth= 3] . ( 4 sec) [ -8984.9530] [ 1989] [depth= 1] . ( 4 sec) [ -8981.5926] [ 1985] [depth= 2] . ( 4 sec) [ -8903.6851] [ 2053] [depth= 1] . ( 5 sec) [ -8852.4718] [ 1985] [depth= 1] . ( 5 sec) [ -8726.2982] [Branch lengths ] . ( 5 sec) [ -8725.3223] [GTR parameters ] . ( 5 sec) [ -8702.3915] [Alpha ][ 0.825869] . ( 6 sec) [ -8514.5244] [ 1924] [depth= 6] . ( 6 sec) [ -8512.1869] [ 1879] [depth= 8] . ( 6 sec) [ -8463.5554] [ 1829] [depth= 1] . ( 6 sec) [ -8414.6309] [ 1804] [depth= 2] . ( 6 sec) [ -8391.3943] [ 1800] [depth= 3] . ( 6 sec) [ -8386.5388] [ 1805] [depth= 1] . ( 6 sec) [ -8386.4791] [ 1808] [depth= 1] . ( 6 sec) [ -8386.1291] [ 1809] [depth= 1] . ( 6 sec) [ -8385.8249] [ 1806] [depth= 2] . ( 7 sec) [ -8366.9463] [ 1804] [depth= 1] . ( 7 sec) [ -8364.0736] [ 1816] [depth= 1] . ( 7 sec) [ -8348.5815] [ 1812] [depth= 2] . ( 7 sec) [ -8345.1775] [ 1808] [depth= 1] . ( 7 sec) [ -8344.4472] [ 1809] [depth= 1] . ( 7 sec) [ -8343.7733] [ 1809] [depth= 1] . ( 7 sec) [ -8341.9730] [ 1808] [depth= 1] . ( 7 sec) [ -8341.5260] [ 1808] [depth= 1] . ( 7 sec) [ -8340.9488] [ 1808] [depth= 1] . ( 8 sec) [ -8340.8524] [ 1807] [depth= 1] . ( 8 sec) [ -8336.2168] [ 1804] [depth= 1] . ( 8 sec) [ -8335.2844] [ 1803] [depth= 1] . ( 8 sec) [ -8334.8283] [ 1804] [depth= 1] . ( 8 sec) [ -8332.7536] [ 1805] [depth= 1] . ( 8 sec) [ -8332.6338] [ 1805] [depth= 1] . ( 8 sec) [ -8331.1617] [ 1806] [depth= 1] . ( 9 sec) [ -8330.6161] [ 1805] [depth= 1] . ( 9 sec) [ -8291.9383] [Branch lengths ] . ( 9 sec) [ -8291.6907] [GTR parameters ] . ( 9 sec) [ -8288.1742] [Alpha ][ 1.016360] . ( 10 sec) [ -8286.3521] [ 1809] [depth= 1] . ( 10 sec) [ -8285.8050] [ 1808] [depth= 1] . ( 11 sec) [ -8285.1599] [ 1808] [depth= 1] . ( 13 sec) [ -8282.5752] [Branch lengths ] . ( 13 sec) [ -8282.5585] [GTR parameters ] . ( 13 sec) [ -8282.5430] [Alpha ][ 1.030952] . ( 17 sec) [ -8281.8408] [Branch lengths ] . ( 37 sec) [ -8281.6956] [Branch lengths ] . ( 37 sec) [ -8281.6956] [Topology ] . ( 38 sec) [ -8281.6899] [Topology ] . ( 39 sec) [ -8281.6886] [Topology ] . ( 40 sec) [ -8281.6882] [Topology ] . ( 40 sec) [ -8281.6863] [GTR parameters ] . ( 40 sec) [ -8281.6852] [Alpha ][ 1.034834] . ( 40 sec) [ -8281.6852] [Topology ] . ( 41 sec) [ -8281.6849] [Topology ] . ( 41 sec) [ -8281.6849] [GTR parameters ] . ( 41 sec) [ -8281.6849] [Alpha ][ 1.034834] . Checking for NNIs, optimizing five branches... . ( 47 sec) [ -8281.6541] [Topology ] . Checking for NNIs, optimizing five branches... . ( 53 sec) [ -8281.6540] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8281.653976. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -23865.9462] [GTR parameters ] . ( 1 sec) [ -23468.1478] [Alpha ][ 0.500960] . ( 1 sec) [ -23381.5441] [ 4264] [depth= 8] . ( 1 sec) [ -23180.2477] [ 4199] [depth= 13] . ( 1 sec) [ -23100.4533] [ 4194] [depth= 4] . ( 1 sec) [ -23029.7335] [ 4194] [depth= 2] . ( 1 sec) [ -22728.8185] [ 4182] [depth= 9] . ( 1 sec) [ -22582.9846] [ 4174] [depth= 4] . ( 1 sec) [ -22393.7286] [ 4132] [depth= 16] . ( 1 sec) [ -22070.7399] [ 4070] [depth= 5] . ( 1 sec) [ -21550.7045] [ 3926] [depth= 14] . ( 2 sec) [ -21350.4184] [ 3848] [depth= 10] . ( 2 sec) [ -21193.7352] [ 3745] [depth= 2] . ( 2 sec) [ -21077.9896] [ 3738] [depth= 2] . ( 2 sec) [ -20668.7477] [ 3627] [depth= 11] . ( 2 sec) [ -20618.6223] [ 3620] [depth= 1] . ( 2 sec) [ -20397.4452] [ 3611] [depth= 2] . ( 2 sec) [ -20182.1922] [ 3524] [depth= 1] . ( 2 sec) [ -20017.3455] [ 3523] [depth= 10] . ( 2 sec) [ -19954.8871] [ 3516] [depth= 9] . ( 2 sec) [ -19656.5163] [ 3386] [depth= 3] . ( 2 sec) [ -19518.3279] [ 3434] [depth= 10] . ( 2 sec) [ -18970.8502] [ 3401] [depth= 4] . ( 2 sec) [ -15168.1437] [ 3386] [depth= 3] . ( 2 sec) [ -14894.8279] [ 3369] [depth= 1] . ( 2 sec) [ -14853.0996] [ 3382] [depth= 1] . ( 2 sec) [ -14631.0294] [ 3315] [depth= 3] . ( 2 sec) [ -14379.5860] [ 3314] [depth= 14] . ( 2 sec) [ -14369.1313] [ 3292] [depth= 1] . ( 2 sec) [ -14234.9966] [ 3290] [depth= 9] . ( 2 sec) [ -14184.4600] [ 3276] [depth= 1] . ( 2 sec) [ -14136.7348] [ 3258] [depth= 5] . ( 2 sec) [ -14043.1392] [ 3242] [depth= 2] . ( 2 sec) [ -13610.6998] [ 3190] [depth= 4] . ( 3 sec) [ -13587.2495] [ 3147] [depth= 3] . ( 3 sec) [ -13553.6293] [ 3144] [depth= 1] . ( 3 sec) [ -13548.3145] [ 3138] [depth= 1] . ( 3 sec) [ -13535.7478] [ 3143] [depth= 1] . ( 3 sec) [ -13392.4935] [ 3063] [depth= 1] . ( 3 sec) [ -13126.9738] [ 3054] [depth= 6] . ( 3 sec) [ -12688.3859] [ 3010] [depth= 4] . ( 3 sec) [ -12685.5302] [ 3013] [depth= 1] . ( 3 sec) [ -12678.5489] [ 3005] [depth= 1] . ( 3 sec) [ -12670.8044] [ 2983] [depth= 1] . ( 3 sec) [ -12405.2716] [ 2850] [depth= 7] . ( 3 sec) [ -12300.3042] [ 2814] [depth= 5] . ( 3 sec) [ -12169.4445] [ 2718] [depth= 7] . ( 3 sec) [ -12166.1590] [ 2694] [depth= 2] . ( 3 sec) [ -12125.0908] [ 2696] [depth= 1] . ( 3 sec) [ -12040.6301] [ 2671] [depth= 3] . ( 3 sec) [ -11964.3291] [ 2662] [depth= 1] . ( 3 sec) [ -11842.7114] [ 2647] [depth= 1] . ( 3 sec) [ -11752.0993] [ 2659] [depth= 1] . ( 3 sec) [ -11718.1706] [ 2633] [depth= 10] . ( 3 sec) [ -11623.9230] [ 2605] [depth= 9] . ( 3 sec) [ -11055.5660] [ 2526] [depth= 5] . ( 4 sec) [ -10819.4436] [ 2465] [depth= 8] . ( 4 sec) [ -10818.1361] [ 2468] [depth= 1] . ( 4 sec) [ -10794.9912] [ 2463] [depth= 3] . ( 4 sec) [ -10790.0383] [ 2452] [depth= 1] . ( 4 sec) [ -10434.0494] [ 2353] [depth= 8] . ( 4 sec) [ -10042.8084] [ 2229] [depth= 2] . ( 4 sec) [ -9917.8242] [ 2200] [depth= 1] . ( 4 sec) [ -9902.4854] [ 2199] [depth= 1] . ( 4 sec) [ -9589.7496] [ 2083] [depth= 2] . ( 4 sec) [ -9585.0882] [ 2088] [depth= 7] . ( 4 sec) [ -9549.6385] [ 2088] [depth= 1] . ( 4 sec) [ -9463.5983] [ 2083] [depth= 3] . ( 4 sec) [ -9320.0036] [ 2036] [depth= 2] . ( 4 sec) [ -9313.4267] [ 2045] [depth= 3] . ( 4 sec) [ -9291.5289] [ 2042] [depth= 1] . ( 4 sec) [ -9287.0133] [ 2052] [depth= 1] . ( 4 sec) [ -9275.6126] [ 2053] [depth= 2] . ( 4 sec) [ -9176.0287] [ 2031] [depth= 6] . ( 4 sec) [ -9172.1246] [ 2029] [depth= 1] . ( 5 sec) [ -9056.5480] [ 2013] [depth= 2] . ( 5 sec) [ -8796.2855] [ 1925] [depth= 1] . ( 5 sec) [ -8795.5258] [ 1927] [depth= 1] . ( 5 sec) [ -8785.1565] [ 1928] [depth= 1] . ( 5 sec) [ -8780.0859] [ 1931] [depth= 1] . ( 5 sec) [ -8746.0432] [ 1934] [depth= 3] . ( 5 sec) [ -8727.3794] [ 1930] [depth= 1] . ( 5 sec) [ -8713.3083] [ 1930] [depth= 1] . ( 5 sec) [ -8697.3209] [ 1888] [depth= 7] . ( 5 sec) [ -8684.0406] [ 1875] [depth= 1] . ( 5 sec) [ -8679.5360] [ 1878] [depth= 1] . ( 5 sec) [ -8453.8584] [Branch lengths ] . ( 6 sec) [ -8451.9682] [GTR parameters ] . ( 6 sec) [ -8424.6862] [Alpha ][ 0.862298] . ( 6 sec) [ -8402.5411] [ 1857] [depth= 12] . ( 6 sec) [ -8402.2889] [ 1857] [depth= 1] . ( 6 sec) [ -8401.7756] [ 1857] [depth= 1] . ( 6 sec) [ -8401.7408] [ 1859] [depth= 1] . ( 6 sec) [ -8378.2616] [ 1854] [depth= 1] . ( 7 sec) [ -8372.5486] [ 1829] [depth= 3] . ( 7 sec) [ -8370.8529] [ 1832] [depth= 1] . ( 7 sec) [ -8370.5160] [ 1829] [depth= 1] . ( 7 sec) [ -8369.6275] [ 1829] [depth= 1] . ( 7 sec) [ -8358.9853] [ 1834] [depth= 1] . ( 7 sec) [ -8356.2885] [ 1843] [depth= 1] . ( 7 sec) [ -8347.9777] [ 1838] [depth= 2] . ( 7 sec) [ -8347.0360] [ 1821] [depth= 2] . ( 7 sec) [ -8345.5831] [ 1818] [depth= 1] . ( 7 sec) [ -8341.6956] [ 1819] [depth= 1] . ( 8 sec) [ -8319.0244] [ 1818] [depth= 2] . ( 8 sec) [ -8318.3919] [ 1817] [depth= 1] . ( 8 sec) [ -8318.2739] [ 1815] [depth= 1] . ( 8 sec) [ -8317.4814] [ 1815] [depth= 1] . ( 8 sec) [ -8316.8946] [ 1814] [depth= 1] . ( 8 sec) [ -8316.2703] [ 1813] [depth= 1] . ( 8 sec) [ -8316.1367] [ 1813] [depth= 1] . ( 8 sec) [ -8315.3958] [ 1813] [depth= 1] . ( 9 sec) [ -8315.1786] [ 1814] [depth= 1] . ( 9 sec) [ -8314.2739] [ 1817] [depth= 1] . ( 9 sec) [ -8314.2629] [ 1817] [depth= 1] . ( 9 sec) [ -8300.2179] [ 1812] [depth= 2] . ( 9 sec) [ -8299.1318] [ 1812] [depth= 1] . ( 9 sec) [ -8298.3263] [ 1812] [depth= 1] . ( 9 sec) [ -8287.1917] [Branch lengths ] . ( 10 sec) [ -8286.9824] [GTR parameters ] . ( 10 sec) [ -8284.6448] [Alpha ][ 1.021077] . ( 10 sec) [ -8284.6075] [ 1812] [depth= 1] . ( 10 sec) [ -8283.8216] [ 1811] [depth= 1] . ( 11 sec) [ -8283.7014] [ 1811] [depth= 1] . ( 12 sec) [ -8283.6824] [ 1811] [depth= 1] . ( 14 sec) [ -8282.2282] [Branch lengths ] . ( 14 sec) [ -8282.2239] [GTR parameters ] . ( 14 sec) [ -8282.2180] [Alpha ][ 1.030044] . ( 15 sec) [ -8282.1507] [ 1808] [depth= 1] . ( 17 sec) [ -8281.7108] [Branch lengths ] . ( 18 sec) [ -8281.7098] [GTR parameters ] . ( 18 sec) [ -8281.7082] [Alpha ][ 1.034615] . ( 38 sec) [ -8281.6914] [Branch lengths ] . ( 38 sec) [ -8281.6914] [Topology ] . ( 39 sec) [ -8281.6895] [Topology ] . ( 40 sec) [ -8281.6888] [Topology ] . ( 40 sec) [ -8281.6887] [GTR parameters ] . ( 40 sec) [ -8281.6887] [Alpha ][ 1.034615] . ( 40 sec) [ -8281.6887] [Topology ] . ( 41 sec) [ -8281.6883] [Topology ] . ( 41 sec) [ -8281.6883] [GTR parameters ] . ( 41 sec) [ -8281.6883] [Alpha ][ 1.034615] . Checking for NNIs, optimizing five branches... . ( 47 sec) [ -8281.6573] [Topology ] . Checking for NNIs, optimizing five branches... . ( 54 sec) [ -8281.6572] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8281.657184. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22868.1866] [GTR parameters ] . ( 1 sec) [ -22511.2462] [Alpha ][ 0.500960] . ( 1 sec) [ -22326.9414] [ 4126] [depth= 9] . ( 1 sec) [ -21813.0712] [ 4050] [depth= 5] . ( 1 sec) [ -21531.6756] [ 3997] [depth= 2] . ( 1 sec) [ -21507.2225] [ 3982] [depth= 1] . ( 1 sec) [ -21290.0611] [ 3917] [depth= 5] . ( 1 sec) [ -21277.6709] [ 3912] [depth= 1] . ( 1 sec) [ -21251.4320] [ 3908] [depth= 2] . ( 1 sec) [ -21232.5713] [ 3902] [depth= 1] . ( 1 sec) [ -21110.6371] [ 3851] [depth= 4] . ( 1 sec) [ -20833.3620] [ 3821] [depth= 4] . ( 2 sec) [ -20796.1708] [ 3818] [depth= 2] . ( 2 sec) [ -20608.6682] [ 3733] [depth= 1] . ( 2 sec) [ -20533.9348] [ 3719] [depth= 4] . ( 2 sec) [ -20502.4590] [ 3717] [depth= 2] . ( 2 sec) [ -20385.1190] [ 3667] [depth= 2] . ( 2 sec) [ -20346.7499] [ 3666] [depth= 1] . ( 2 sec) [ -20285.4150] [ 3622] [depth= 1] . ( 2 sec) [ -20196.6583] [ 3619] [depth= 4] . ( 2 sec) [ -20146.4650] [ 3607] [depth= 3] . ( 2 sec) [ -19978.0197] [ 3577] [depth= 7] . ( 2 sec) [ -19784.3453] [ 3543] [depth= 8] . ( 2 sec) [ -19122.4719] [ 3552] [depth= 2] . ( 2 sec) [ -18850.3861] [ 3471] [depth= 11] . ( 2 sec) [ -15511.3906] [ 3485] [depth= 1] . ( 2 sec) [ -15023.8028] [ 3424] [depth= 2] . ( 2 sec) [ -14450.8540] [ 3351] [depth= 9] . ( 2 sec) [ -14126.9823] [ 3284] [depth= 9] . ( 2 sec) [ -13995.6695] [ 3181] [depth= 8] . ( 2 sec) [ -13984.3461] [ 3165] [depth= 2] . ( 2 sec) [ -13928.2845] [ 3174] [depth= 1] . ( 2 sec) [ -13751.2775] [ 3162] [depth= 7] . ( 2 sec) [ -13694.8151] [ 3141] [depth= 3] . ( 2 sec) [ -13585.4653] [ 3119] [depth= 5] . ( 2 sec) [ -13349.3179] [ 3063] [depth= 4] . ( 3 sec) [ -13030.1537] [ 2918] [depth= 6] . ( 3 sec) [ -12885.2326] [ 2880] [depth= 1] . ( 3 sec) [ -12878.8913] [ 2878] [depth= 1] . ( 3 sec) [ -12869.5540] [ 2878] [depth= 3] . ( 3 sec) [ -12384.2229] [ 2852] [depth= 4] . ( 3 sec) [ -12279.8851] [ 2841] [depth= 1] . ( 3 sec) [ -12252.9858] [ 2846] [depth= 1] . ( 3 sec) [ -12045.8656] [ 2780] [depth= 2] . ( 3 sec) [ -12008.4120] [ 2777] [depth= 2] . ( 3 sec) [ -11962.5763] [ 2762] [depth= 1] . ( 3 sec) [ -11666.6689] [ 2785] [depth= 9] . ( 3 sec) [ -11522.0648] [ 2778] [depth= 2] . ( 3 sec) [ -11514.3973] [ 2778] [depth= 1] . ( 3 sec) [ -11362.1055] [ 2766] [depth= 3] . ( 3 sec) [ -11248.9743] [ 2765] [depth= 2] . ( 3 sec) [ -11141.9368] [ 2618] [depth= 6] . ( 3 sec) [ -10828.0702] [ 2614] [depth= 3] . ( 3 sec) [ -10514.9656] [ 2504] [depth= 1] . ( 3 sec) [ -10456.7051] [ 2507] [depth= 1] . ( 3 sec) [ -10108.2003] [ 2390] [depth= 5] . ( 3 sec) [ -10104.1176] [ 2390] [depth= 1] . ( 4 sec) [ -10067.9480] [ 2381] [depth= 3] . ( 4 sec) [ -10031.8943] [ 2381] [depth= 1] . ( 4 sec) [ -10024.1165] [ 2381] [depth= 1] . ( 4 sec) [ -10013.8940] [ 2380] [depth= 1] . ( 4 sec) [ -10000.4277] [ 2373] [depth= 2] . ( 4 sec) [ -9858.4004] [ 2305] [depth= 5] . ( 4 sec) [ -9780.6377] [ 2289] [depth= 2] . ( 4 sec) [ -9772.3118] [ 2263] [depth= 4] . ( 4 sec) [ -9498.7773] [ 2256] [depth= 1] . ( 4 sec) [ -9312.2815] [ 2153] [depth= 10] . ( 4 sec) [ -9227.3011] [ 2140] [depth= 1] . ( 4 sec) [ -9180.8484] [ 2133] [depth= 1] . ( 4 sec) [ -9162.3797] [ 2131] [depth= 1] . ( 4 sec) [ -9137.7012] [ 2105] [depth= 5] . ( 4 sec) [ -9015.9341] [ 2076] [depth= 5] . ( 4 sec) [ -8909.3421] [ 2031] [depth= 3] . ( 4 sec) [ -8899.3096] [ 2021] [depth= 1] . ( 4 sec) [ -8897.3986] [ 2021] [depth= 1] . ( 4 sec) [ -8890.8641] [ 2020] [depth= 1] . ( 5 sec) [ -8733.1044] [ 1907] [depth= 4] . ( 5 sec) [ -8648.8961] [ 1855] [depth= 1] . ( 5 sec) [ -8629.1595] [ 1849] [depth= 2] . ( 5 sec) [ -8626.7430] [ 1854] [depth= 1] . ( 5 sec) [ -8620.1810] [ 1849] [depth= 1] . ( 5 sec) [ -8604.0449] [ 1854] [depth= 1] . ( 5 sec) [ -8603.2040] [ 1856] [depth= 1] . ( 5 sec) [ -8471.9445] [Branch lengths ] . ( 6 sec) [ -8470.2462] [GTR parameters ] . ( 6 sec) [ -8440.6354] [Alpha ][ 0.892275] . ( 6 sec) [ -8434.8791] [ 1852] [depth= 7] . ( 6 sec) [ -8430.9434] [ 1863] [depth= 1] . ( 6 sec) [ -8420.1746] [ 1862] [depth= 1] . ( 6 sec) [ -8419.5074] [ 1856] [depth= 2] . ( 6 sec) [ -8419.3737] [ 1856] [depth= 1] . ( 6 sec) [ -8413.9872] [ 1860] [depth= 1] . ( 6 sec) [ -8359.6791] [ 1856] [depth= 1] . ( 7 sec) [ -8355.6437] [ 1853] [depth= 1] . ( 7 sec) [ -8354.7181] [ 1856] [depth= 1] . ( 7 sec) [ -8344.9591] [ 1844] [depth= 1] . ( 7 sec) [ -8344.6592] [ 1842] [depth= 1] . ( 7 sec) [ -8334.6050] [ 1834] [depth= 1] . ( 7 sec) [ -8333.5216] [ 1831] [depth= 1] . ( 7 sec) [ -8329.1320] [ 1825] [depth= 1] . ( 7 sec) [ -8328.5575] [ 1825] [depth= 1] . ( 7 sec) [ -8327.1991] [ 1827] [depth= 1] . ( 8 sec) [ -8326.9342] [ 1825] [depth= 1] . ( 8 sec) [ -8326.6253] [ 1826] [depth= 1] . ( 8 sec) [ -8326.1391] [ 1826] [depth= 1] . ( 8 sec) [ -8325.4637] [ 1827] [depth= 1] . ( 8 sec) [ -8323.6737] [ 1829] [depth= 1] . ( 8 sec) [ -8317.1204] [ 1812] [depth= 1] . ( 8 sec) [ -8315.7193] [ 1813] [depth= 1] . ( 9 sec) [ -8315.1368] [ 1812] [depth= 1] . ( 9 sec) [ -8312.8877] [ 1811] [depth= 1] . ( 9 sec) [ -8287.8955] [Branch lengths ] . ( 10 sec) [ -8287.7503] [GTR parameters ] . ( 10 sec) [ -8286.4110] [Alpha ][ 1.014399] . ( 10 sec) [ -8285.0744] [ 1811] [depth= 1] . ( 10 sec) [ -8284.9643] [ 1811] [depth= 1] . ( 11 sec) [ -8284.8202] [ 1808] [depth= 1] . ( 13 sec) [ -8282.6476] [Branch lengths ] . ( 14 sec) [ -8282.6366] [GTR parameters ] . ( 14 sec) [ -8282.6152] [Alpha ][ 1.031510] . ( 17 sec) [ -8281.9803] [Branch lengths ] . ( 37 sec) [ -8281.7036] [Branch lengths ] . ( 37 sec) [ -8281.7036] [Topology ] . ( 38 sec) [ -8281.6899] [Topology ] . ( 39 sec) [ -8281.6881] [Topology ] . ( 40 sec) [ -8281.6876] [Topology ] . ( 40 sec) [ -8281.6863] [GTR parameters ] . ( 40 sec) [ -8281.6854] [Alpha ][ 1.034901] . ( 40 sec) [ -8281.6854] [Topology ] . ( 41 sec) [ -8281.6852] [Topology ] . ( 41 sec) [ -8281.6852] [GTR parameters ] . ( 41 sec) [ -8281.6852] [Alpha ][ 1.034901] . Checking for NNIs, optimizing five branches... . ( 48 sec) [ -8281.6846] [Topology ] . Checking for NNIs, optimizing five branches... . ( 54 sec) [ -8281.6842] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8281.684174. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -23646.3280] [GTR parameters ] . ( 1 sec) [ -23251.1827] [Alpha ][ 0.500960] . ( 1 sec) [ -23192.8853] [ 4269] [depth= 7] . ( 1 sec) [ -22968.2055] [ 4223] [depth= 10] . ( 1 sec) [ -22806.0628] [ 4215] [depth= 6] . ( 1 sec) [ -22723.5844] [ 4210] [depth= 1] . ( 1 sec) [ -19186.6561] [ 4138] [depth= 12] . ( 1 sec) [ -18849.5264] [ 4139] [depth= 6] . ( 1 sec) [ -18674.5815] [ 4112] [depth= 4] . ( 1 sec) [ -18480.3895] [ 4106] [depth= 1] . ( 1 sec) [ -18215.3196] [ 3983] [depth= 7] . ( 1 sec) [ -17845.0321] [ 3936] [depth= 9] . ( 1 sec) [ -17673.4963] [ 3907] [depth= 1] . ( 1 sec) [ -17330.3403] [ 3883] [depth= 17] . ( 1 sec) [ -17130.5283] [ 3813] [depth= 11] . ( 1 sec) [ -16915.3271] [ 3724] [depth= 1] . ( 1 sec) [ -16641.0230] [ 3714] [depth= 5] . ( 1 sec) [ -16532.2078] [ 3690] [depth= 10] . ( 1 sec) [ -16454.5835] [ 3584] [depth= 2] . ( 1 sec) [ -16019.5833] [ 3576] [depth= 4] . ( 1 sec) [ -15709.1632] [ 3574] [depth= 2] . ( 1 sec) [ -15702.0868] [ 3559] [depth= 9] . ( 1 sec) [ -15490.3270] [ 3420] [depth= 3] . ( 1 sec) [ -15113.4813] [ 3387] [depth= 3] . ( 2 sec) [ -14915.0297] [ 3298] [depth= 10] . ( 2 sec) [ -14798.7919] [ 3294] [depth= 1] . ( 2 sec) [ -14744.2116] [ 3275] [depth= 3] . ( 2 sec) [ -14721.3845] [ 3276] [depth= 1] . ( 2 sec) [ -14534.5324] [ 3256] [depth= 3] . ( 2 sec) [ -14378.7828] [ 3255] [depth= 1] . ( 2 sec) [ -14378.4173] [ 3260] [depth= 1] . ( 2 sec) [ -13963.8980] [ 3078] [depth= 14] . ( 2 sec) [ -13963.7665] [ 3076] [depth= 1] . ( 2 sec) [ -13899.1836] [ 3046] [depth= 1] . ( 2 sec) [ -13710.8019] [ 3021] [depth= 2] . ( 2 sec) [ -13625.5612] [ 3012] [depth= 1] . ( 2 sec) [ -13619.9661] [ 3021] [depth= 1] . ( 2 sec) [ -13322.6161] [ 2970] [depth= 9] . ( 2 sec) [ -13208.0870] [ 2934] [depth= 13] . ( 2 sec) [ -12953.5144] [ 2872] [depth= 2] . ( 2 sec) [ -12620.1589] [ 2766] [depth= 6] . ( 2 sec) [ -12081.8047] [ 2729] [depth= 1] . ( 2 sec) [ -11740.4118] [ 2710] [depth= 5] . ( 2 sec) [ -11651.0770] [ 2703] [depth= 6] . ( 2 sec) [ -11617.6288] [ 2695] [depth= 1] . ( 2 sec) [ -11528.2861] [ 2727] [depth= 1] . ( 2 sec) [ -11510.3722] [ 2728] [depth= 1] . ( 3 sec) [ -11361.3984] [ 2659] [depth= 1] . ( 3 sec) [ -10979.9856] [ 2652] [depth= 4] . ( 3 sec) [ -10868.7215] [ 2591] [depth= 7] . ( 3 sec) [ -10853.4160] [ 2583] [depth= 2] . ( 3 sec) [ -10830.6184] [ 2582] [depth= 1] . ( 3 sec) [ -10820.3946] [ 2586] [depth= 1] . ( 3 sec) [ -10817.5310] [ 2591] [depth= 1] . ( 3 sec) [ -10613.0412] [ 2528] [depth= 6] . ( 3 sec) [ -10581.7257] [ 2515] [depth= 4] . ( 3 sec) [ -10509.2435] [ 2492] [depth= 2] . ( 3 sec) [ -10324.8547] [ 2431] [depth= 5] . ( 3 sec) [ -10281.6181] [ 2416] [depth= 1] . ( 3 sec) [ -10234.4438] [ 2358] [depth= 2] . ( 3 sec) [ -10183.9401] [ 2325] [depth= 7] . ( 3 sec) [ -10133.8998] [ 2329] [depth= 5] . ( 3 sec) [ -9865.4008] [ 2212] [depth= 5] . ( 3 sec) [ -9837.0896] [ 2217] [depth= 1] . ( 3 sec) [ -9638.0766] [ 2174] [depth= 4] . ( 3 sec) [ -9619.7222] [ 2170] [depth= 1] . ( 3 sec) [ -9390.9739] [ 2141] [depth= 1] . ( 3 sec) [ -9377.0368] [ 2141] [depth= 1] . ( 3 sec) [ -9364.7961] [ 2141] [depth= 1] . ( 3 sec) [ -9353.1352] [ 2137] [depth= 1] . ( 4 sec) [ -9312.1183] [ 2129] [depth= 3] . ( 4 sec) [ -9285.9843] [ 2088] [depth= 4] . ( 4 sec) [ -9179.9627] [ 2075] [depth= 2] . ( 4 sec) [ -9174.6782] [ 2076] [depth= 1] . ( 4 sec) [ -9159.6670] [ 2062] [depth= 1] . ( 4 sec) [ -9155.0716] [ 2058] [depth= 1] . ( 4 sec) [ -9033.8612] [ 2040] [depth= 2] . ( 4 sec) [ -8925.3434] [ 1991] [depth= 2] . ( 4 sec) [ -8813.0089] [ 1912] [depth= 1] . ( 4 sec) [ -8802.0621] [ 1949] [depth= 1] . ( 4 sec) [ -8738.0284] [ 1937] [depth= 2] . ( 4 sec) [ -8737.9761] [ 1938] [depth= 1] . ( 4 sec) [ -8727.9198] [ 1926] [depth= 2] . ( 4 sec) [ -8727.8565] [ 1903] [depth= 1] . ( 4 sec) [ -8709.4086] [ 1865] [depth= 3] . ( 4 sec) [ -8702.8101] [ 1870] [depth= 1] . ( 4 sec) [ -8693.4752] [ 1868] [depth= 1] . ( 5 sec) [ -8550.3647] [ 1839] [depth= 1] . ( 5 sec) [ -8399.1081] [Branch lengths ] . ( 5 sec) [ -8398.4859] [GTR parameters ] . ( 5 sec) [ -8364.6169] [Alpha ][ 0.930230] . ( 5 sec) [ -8356.2947] [ 1834] [depth= 3] . ( 6 sec) [ -8356.2583] [ 1835] [depth= 1] . ( 6 sec) [ -8351.4412] [ 1828] [depth= 2] . ( 6 sec) [ -8336.4425] [ 1821] [depth= 2] . ( 6 sec) [ -8319.7449] [ 1807] [depth= 1] . ( 6 sec) [ -8319.4344] [ 1808] [depth= 1] . ( 6 sec) [ -8318.6561] [ 1808] [depth= 1] . ( 6 sec) [ -8318.5049] [ 1808] [depth= 1] . ( 6 sec) [ -8318.3379] [ 1808] [depth= 1] . ( 7 sec) [ -8309.5162] [ 1813] [depth= 1] . ( 7 sec) [ -8304.5767] [ 1824] [depth= 1] . ( 7 sec) [ -8304.4876] [ 1824] [depth= 1] . ( 7 sec) [ -8300.6102] [ 1818] [depth= 1] . ( 7 sec) [ -8300.1915] [ 1817] [depth= 1] . ( 7 sec) [ -8298.9443] [ 1817] [depth= 1] . ( 7 sec) [ -8298.8213] [ 1817] [depth= 1] . ( 8 sec) [ -8298.6635] [ 1816] [depth= 1] . ( 8 sec) [ -8297.0047] [ 1812] [depth= 1] . ( 8 sec) [ -8296.8303] [ 1812] [depth= 1] . ( 8 sec) [ -8296.4466] [ 1811] [depth= 1] . ( 8 sec) [ -8296.3699] [ 1811] [depth= 1] . ( 9 sec) [ -8293.7063] [ 1811] [depth= 1] . ( 9 sec) [ -8291.5748] [ 1811] [depth= 1] . ( 9 sec) [ -8284.3302] [Branch lengths ] . ( 10 sec) [ -8284.2560] [GTR parameters ] . ( 10 sec) [ -8283.4907] [Alpha ][ 1.025033] . ( 10 sec) [ -8282.8984] [ 1811] [depth= 1] . ( 12 sec) [ -8282.7081] [ 1808] [depth= 1] . ( 13 sec) [ -8281.7984] [Branch lengths ] . ( 14 sec) [ -8281.7758] [GTR parameters ] . ( 14 sec) [ -8281.7691] [Alpha ][ 1.034641] . ( 17 sec) [ -8281.6937] [Branch lengths ] . ( 38 sec) [ -8281.6872] [Branch lengths ] . ( 38 sec) [ -8281.6872] [Topology ] . ( 38 sec) [ -8281.6865] [Topology ] . ( 38 sec) [ -8281.6864] [GTR parameters ] . ( 38 sec) [ -8281.6864] [Alpha ][ 1.034641] . Checking for NNIs, optimizing five branches... . ( 45 sec) [ -8281.6859] [Topology ] . Checking for NNIs, optimizing five branches... . ( 51 sec) [ -8281.6857] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8281.685703. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-8350.364615 . ( 1 sec) [ -8348.2932] [GTR parameters ] . ( 1 sec) [ -8348.1523] [Alpha ][ 1.044806] . ( 1 sec) [ -8348.1523] [Topology ] . ( 2 sec) [ -8296.9542] [Topology ] . ( 3 sec) [ -8286.8915] [Topology ] . ( 4 sec) [ -8284.3275] [Topology ] . ( 4 sec) [ -8282.5314] [Topology ] . ( 5 sec) [ -8282.0722] [Topology ] . ( 6 sec) [ -8281.8788] [Topology ] . ( 7 sec) [ -8281.7891] [Topology ] . ( 7 sec) [ -8281.7461] [Topology ] . ( 8 sec) [ -8281.7251] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8281.725051 . ( 15 sec) [ -8281.6764] [GTR parameters ] . ( 15 sec) [ -8281.6695] [Alpha ][ 1.034679] . ( 15 sec) [ -8281.6695] [Topology ] . ( 16 sec) [ -8281.6579] [Topology ] . ( 17 sec) [ -8281.6524] [Topology ] . ( 17 sec) [ -8281.6496] [Topology ] . ( 18 sec) [ -8281.6482] [Topology ] . ( 19 sec) [ -8281.6475] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8281.647510 . ( 25 sec) [ -8281.6474] [GTR parameters ] . ( 25 sec) [ -8281.6474] [Alpha ][ 1.034679] . ( 25 sec) [ -8281.6474] [Topology ] . ( 26 sec) [ -8281.6470] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 39 sec) [ -8348.2932] [GTR parameters ] . ( 39 sec) [ -8348.1523] [Alpha ][ 1.044806] . ( 39 sec) [ -8345.9422] [ 1799] [depth= 1] . ( 39 sec) [ -8342.9652] [ 1804] [depth= 1] . ( 39 sec) [ -8340.3662] [ 1799] [depth= 1] . ( 39 sec) [ -8329.5668] [ 1811] [depth= 1] . ( 40 sec) [ -8327.5249] [ 1812] [depth= 1] . ( 40 sec) [ -8325.0888] [ 1812] [depth= 1] . ( 40 sec) [ -8324.0027] [ 1811] [depth= 1] . ( 40 sec) [ -8323.8872] [ 1812] [depth= 1] . ( 40 sec) [ -8323.2903] [ 1812] [depth= 1] . ( 40 sec) [ -8321.7625] [ 1810] [depth= 1] . ( 40 sec) [ -8317.9600] [ 1812] [depth= 1] . ( 40 sec) [ -8312.2771] [ 1807] [depth= 1] . ( 40 sec) [ -8312.1923] [ 1811] [depth= 1] . ( 40 sec) [ -8311.2178] [ 1807] [depth= 1] . ( 40 sec) [ -8311.1213] [ 1811] [depth= 1] . ( 41 sec) [ -8308.7561] [ 1809] [depth= 2] . ( 41 sec) [ -8307.9129] [ 1809] [depth= 1] . ( 41 sec) [ -8300.6023] [ 1809] [depth= 1] . ( 42 sec) [ -8282.8520] [Branch lengths ] . ( 43 sec) [ -8282.8017] [GTR parameters ] . ( 43 sec) [ -8282.7776] [Alpha ][ 1.027091] . ( 43 sec) [ -8282.7041] [ 1808] [depth= 1] . ( 46 sec) [ -8281.8116] [Branch lengths ] . ( 46 sec) [ -8281.8111] [GTR parameters ] . ( 47 sec) [ -8281.8087] [Alpha ][ 1.032721] . ( 67 sec) [ -8281.7002] [Branch lengths ] . ( 67 sec) [ -8281.7002] [Topology ] . ( 68 sec) [ -8281.6911] [Topology ] . ( 69 sec) [ -8281.6880] [Topology ] . ( 69 sec) [ -8281.6865] [Topology ] . ( 70 sec) [ -8281.6858] [Topology ] . ( 70 sec) [ -8281.6858] [GTR parameters ] . ( 70 sec) [ -8281.6854] [Alpha ][ 1.034755] . ( 70 sec) [ -8281.6854] [Topology ] . ( 71 sec) [ -8281.6850] [Topology ] . ( 71 sec) [ -8281.6850] [GTR parameters ] . ( 71 sec) [ -8281.6850] [Alpha ][ 1.034755] . Checking for NNIs, optimizing five branches... . ( 78 sec) [ -8281.6543] [Topology ] . Checking for NNIs, optimizing five branches... . ( 84 sec) [ -8281.6541] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8281.646982 . Log likelihood obtained after SPR moves : -8281.654128 . Log likelihood of the current tree: -8281.646982. . Printing the most likely tree in file 'data18.phy_phyml_tree.txt'... . Best log likelihood : -8281.646982 . Time used 0h1m31s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo